Locus 9782

Sequence ID	3R_DroMel_CAF1
Location	25,957,485 – 25,957,595
Length	110
Max. P	0.880408

overview

Window 4

Location	25,957,485 – 25,957,595
Length	110
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	76.67
Mean single sequence MFE	-29.62
Consensus MFE	-18.72
Energy contribution	-19.25
Covariance contribution	0.53
Combinations/Pair	1.32
Mean z-score	-1.58
Structure conservation index	0.63
SVM decision value	0.67
SVM RNA-class probability	0.818465
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25957485 110 + 27905053
GGUUAACACCACUUACUUUAUAUCCGGUGAAGCGGAGCUGAUCUUUAGGAGUAGCUCCACCUCACCCACUCGGUCGUUCUUAGGCCCUUUGGUCAGUUGAACUGUAACAC
.((((..((((..............(((((.(.(((((((.((.....)).))))))).).))))).....((((.......))))...))))(((.....))))))).. ( -32.60)
>DroVir_CAF1 14873 104 + 1
UUCUGUUACUACUUACUCCAGAUCCGGAUCGGUAGAGCUGAACUUGAUGUUAAUGUCUACGGUAGCUACGCGCU---UCUU--GUUCUUCUG-CAACUCGACGCUGAUAA
(((.(((.(((((...(((......)))..)))))))).))).....(((((.((((...((.(((.....)))---))((--((......)-)))...)))).))))). ( -19.70)
>DroSec_CAF1 9686 110 + 1
GGUUAACACUACUUACUUUAUAUCCGGUGAAGCGGAGCUGAUCUUCAGGAGUAGCUCCACCUCACCCACUCGGUCGUUCAUAGGCCCUUUGGUCAGUUUAACUGUAACAU
((((((.((((((............(((((.(.(((((((.((.....)).))))))).).))))).....((((.......))))....))).)))))))))....... ( -32.30)
>DroSim_CAF1 9674 110 + 1
GGUUAACACUACUUACUUUAUAUCCGGUGAAGCGGAGCUGAUCUUCAGGAGUAGCUCCACCUCACCCACUCGGUCGUUCUUUGGCCCUUUGGUCAGUUUAACUGUAACAU
((((((.((((((............(((((.(.(((((((.((.....)).))))))).).))))).....(((((.....)))))....))).)))))))))....... ( -32.90)
>DroEre_CAF1 7692 110 + 1
GGUGACCACUACUUACUUUAUAUCCGGCGGCGCGGAGCUGAUCUUCAAGAUAAGCUCCACCUCACCCACUCUGUCCUGCUUAGGUCCUUUGGUCAGCUUAACCACAACAU
(.((((((.................((.((.(.((((((.(((.....))).)))))).).)).))......(.(((....))).)...)))))).)............. ( -28.20)
>DroYak_CAF1 7773 106 + 1
----ACCACUACUUACUUUAUUUCCGGUGGAGCGGAGCUGAUCUUCAAGAGCAGCUCCACCUCACCCACUCUGUCGGCCUUGGGCCCUUUGGUCAGCUUAACUGUAACAU
----((((.................((((..(.(((((((.((.....)).))))))).)..)))).........((((...))))...))))(((.....)))...... ( -32.00)
>consensus
GGUUAACACUACUUACUUUAUAUCCGGUGAAGCGGAGCUGAUCUUCAGGAGUAGCUCCACCUCACCCACUCGGUCGUUCUUAGGCCCUUUGGUCAGCUUAACUGUAACAU
.........................(((((.(.(((((((.((.....)).))))))).).)))))................((((....))))................ (-18.72 = -19.25 +   0.53)

alignment

secondary structure

dotplot

Window 5

Location	25,957,485 – 25,957,595
Length	110
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	76.67
Mean single sequence MFE	-32.66
Consensus MFE	-22.57
Energy contribution	-23.22
Covariance contribution	0.65
Combinations/Pair	1.46
Mean z-score	-1.50
Structure conservation index	0.69
SVM decision value	0.91
SVM RNA-class probability	0.880408
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25957485 110 - 27905053
GUGUUACAGUUCAACUGACCAAAGGGCCUAAGAACGACCGAGUGGGUGAGGUGGAGCUACUCCUAAAGAUCAGCUCCGCUUCACCGGAUAUAAAGUAAGUGGUGUUAACC
..(((((((.....)))((((..((............)).....((((((((((((((..((.....))..))))))))))))))..............))))..)))). ( -34.80)
>DroVir_CAF1 14873 104 - 1
UUAUCAGCGUCGAGUUG-CAGAAGAAC--AAGA---AGCGCGUAGCUACCGUAGACAUUAACAUCAAGUUCAGCUCUACCGAUCCGGAUCUGGAGUAAGUAGUAACAGAA
...((.((((....(((-........)--))..---.))))((.(((((.(((((....(((.....)))....)))))...((((....))))....))))).)).)). ( -19.50)
>DroSec_CAF1 9686 110 - 1
AUGUUACAGUUAAACUGACCAAAGGGCCUAUGAACGACCGAGUGGGUGAGGUGGAGCUACUCCUGAAGAUCAGCUCCGCUUCACCGGAUAUAAAGUAAGUAGUGUUAACC
......(((.....))).......(((((((..((.......(.((((((((((((((..((.....))..)))))))))))))).).......))..)))).))).... ( -35.34)
>DroSim_CAF1 9674 110 - 1
AUGUUACAGUUAAACUGACCAAAGGGCCAAAGAACGACCGAGUGGGUGAGGUGGAGCUACUCCUGAAGAUCAGCUCCGCUUCACCGGAUAUAAAGUAAGUAGUGUUAACC
........(((((((((..((..((............))...))((((((((((((((..((.....))..))))))))))))))..............)))).))))). ( -33.40)
>DroEre_CAF1 7692 110 - 1
AUGUUGUGGUUAAGCUGACCAAAGGACCUAAGCAGGACAGAGUGGGUGAGGUGGAGCUUAUCUUGAAGAUCAGCUCCGCGCCGCCGGAUAUAAAGUAAGUAGUGGUCACC
......(((((.....)))))...((((...((...((....(.((((..((((((((.(((.....))).))))))))..)))).).......))..))...))))... ( -33.50)
>DroYak_CAF1 7773 106 - 1
AUGUUACAGUUAAGCUGACCAAAGGGCCCAAGGCCGACAGAGUGGGUGAGGUGGAGCUGCUCUUGAAGAUCAGCUCCGCUCCACCGGAAAUAAAGUAAGUAGUGGU----
......(((.....)))((((...((((...)))).........((((..(((((((((.((.....)).)))))))))..)))).................))))---- ( -39.40)
>consensus
AUGUUACAGUUAAACUGACCAAAGGGCCUAAGAACGACCGAGUGGGUGAGGUGGAGCUACUCCUGAAGAUCAGCUCCGCUUCACCGGAUAUAAAGUAAGUAGUGUUAACC
(((((.(((.....)))...........................((((((((((((((..((.....))..)))))))))))))).)))))................... (-22.57 = -23.22 +   0.65)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:42:04 2006